How can I draw an alpha-channel, or clone one texture over the other in Texture Paint mode in Cycles?
This is not cycles or Blender internal dependant, this is just texture paint mode. So the principle is the same. You can clone the same way.

You can also "erase alpha" (blend method in the "texture paint mode" tools panel). But this will not "unclone" the original textures.

If you want to erase part of one texture, clone again the other one instead of erasing using alpha.